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A multiplex pharmacogenetics assay using the MinION nanopore sequencing device.
Liau, Yusmiati; Cree, Simone L; Maggo, Simran; Miller, Allison L; Pearson, John F; Gladding, Patrick A; Kennedy, Martin A.
Afiliación
  • Liau Y; Department of Pathology and Biomedical Science, University of Otago, Christchurch.
  • Cree SL; Department of Pathology and Biomedical Science, University of Otago, Christchurch.
  • Maggo S; Department of Pathology and Biomedical Science, University of Otago, Christchurch.
  • Miller AL; Department of Pathology and Biomedical Science, University of Otago, Christchurch.
  • Pearson JF; Department of Pathology and Biomedical Science, University of Otago, Christchurch.
  • Gladding PA; Theranostics Laboratory, North Shore Hospital, Shakespeare Rd, Auckland, New Zealand.
  • Kennedy MA; Department of Pathology and Biomedical Science, University of Otago, Christchurch.
Pharmacogenet Genomics ; 29(9): 207-215, 2019 11.
Article en En | MEDLINE | ID: mdl-31568131
OBJECTIVES: The MinION nanopore sequencing device opens the opportunity to cost-effective and point-of-care DNA sequencing. As a proof of principle, we developed a multiplex assay targeting pharmacogenetic variants related to clopidogrel and warfarin, the two commonly used drugs that show response variability due to genetic polymorphisms. METHODS: Six reference and 78 clinical DNA samples were amplified by PCR to generate 15 amplicons targeting 27 key variants. These products were then barcoded to enable sample multiplexing in one sequencing run. Four variant calling tools (marginCaller, VarScan 2, nanopolish, Clairvoyante) were used to compare genotyping accuracy. RESULTS: In our cohort, 81 out of 84 samples were successfully sequenced and genotyped. Using nanopolish as the variant calling tool achieved accuracy >95% for all except two variants. A known single base deletion (CYP2C9*6) was successfully detected. CONCLUSION: While minor misgenotyping issues exist, this work demonstrates that drug-specific or broad pharmacogenetic screening assays using small PCR amplicons are possible on the MinION sequencing device.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Farmacogenética / Secuenciación de Nanoporos Límite: Humans Idioma: En Revista: Pharmacogenet Genomics Asunto de la revista: FARMACOLOGIA / GENETICA MEDICA Año: 2019 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
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XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Farmacogenética / Secuenciación de Nanoporos Límite: Humans Idioma: En Revista: Pharmacogenet Genomics Asunto de la revista: FARMACOLOGIA / GENETICA MEDICA Año: 2019 Tipo del documento: Article Pais de publicación: Estados Unidos